Having trailed to a third minute James Armson effort, City had Paul Farman and some poor finishing from the visitors to thank in an opening period which was dominated by Nuneaton; Farman superbly denying Wesley York whilst Daniel Sleath fired wide with only Farman to beat as the half wore on.
Whilst the opening half was all Town, the second period was all City with the pressure paying off in the 73rd minute as, after Vadaine Oliver was upended by James Forsdick, the Nuneaton man was dismissed as the last man before substitute Nicky Nicolau drilled powerfully past Neil Collett from the resultant free-kick.
With the game in its last 10 minutes a Nicolau free-kick led to a City corner and when the flag-kick was played in deep, there at the back post was Tom Miller to bundle home from close range for what turned out to be the winner.
There was still time for Colin Larkin to be denied by defender Gavin Cowan on the line whilst a stoppage-time penalty miss by fellow substitute Jamie Taylor didn't prove costly with the game already wrapped up.
Teenager Conner Robinson was handed his full debut and Tom Miller and Adam Smith both returned to the starting-line-up for this Blue Square Bet Premier game against Nuneaton Town at The 12th Imp Sincil Bank Stadium.
With Gary Mills suspended following his sending off at Tamworth, the captain's armband went to John Nutter and after he and his counterpart Gareth Dean tossed up play started with the Imps kicking off.
It was a cagey opening to the game but it sprung into life in the third minute when a low cross from the Nuneaton left was allowed to run through to James Armson and he duly drilled powerfully past Paul Farman and into the roof of the net from just inside the box.
City looked for a quick response with Jake Sheridan winning a corner two minutes later but when David Morgan's delivery fell to Mamadou Fofana the French midfielder saw his 25-yard effort go well wide.
Nuneaton's next attack saw Miller go in hard on Wesley York and once the ball had gone out of play referee Chris Knowles, who had initially allowed play to carry on, produced a yellow card for the returning City defender.
At the other end Dan Gray drilled a low effort into Neil Collett's gloves after his throw-in was played back to him and as Nuneaton responded a slip by Nutter gave Adam Walker the chance to cross to York but he was denied by Farman who pulled off a superb save to keep the score at 0-1.
Farman was then forced sprint off his line and punch clear under pressure from Andy Brown after Andrew Boyce failed to get any purchase on a header back to his keeper. City's reply saw good work from Robinson and Sheridan create a change for Vadaine Oliver but his goalbound header was well held by Collett.
Midway through the opening period referee Knowles earned the wrath of the City crowd after penalising Sheridan for a foul when the Imps' man went down in the Town box. Oliver was then denied again by Collett following a sweeping move down the right.
A quiet spell ensued before Morgan was left grounded by Ben Ford in a challenge which Mr Knowles deemed fair. When the ball went out for a throw-in, physio Sam Rees was able to administer treatment to the teenage midfielder.
Five minutes before the break Oliver beat Collett to a Gray ball into the box only to see his header go behind for a goal-kick whilst at the other end Farman was forced to sprint back and claim a prodded York effort before it trickled over the line.
Daniel Sleath then wasted a glorious chance to double his team's advantage after the midfielder found himself in space on the edge of the City box only to finish poorly with the ball going well wide. The Imps' response saw Smith win an unproductive corner as the Fourth Official indicated that a minimum of two minutes were to be added on.
HT: Imps 0 Nuneaton 1
The visitors restarted proceedings as both sides emerged unchanged but it was the Imps who were quickly out of the traps with some excellent play by Robinson down the left seeing him create an opportunity for Sheridan only for Collett to fling himself full length to tip his effort behind for a corner.
Ben Ford picked up a 51st minute caution for a late challenge on Smith with the resultant free-kick leading to another corner as the Imps stepped thing up again. Shortly afterwards Morgan tested Collett with a rasping 25-yard drive.
City had to be on their guard, however, as Town won their first corner of the game in the 56th minute which was fortunately wasted. At the other end Oliver was denied by the back-tracking Simon Forsdick after latching on to a Robinson flick-on.
The game was becoming somewhat scrappy with a number of free-kicks being conceded either side of the hour mark. From one, Andrew Boyce was booked for a foul on Ford before a treble City change saw Jamie Taylor, Nicky Nicolau and Colin Larkin come on for Conner Robinson, Jake Sheridan and Adam Smith.
A couple of minutes later Farman was forced to go down low to claim a Daniel Sleath shot. Sleath was then upended by a sliding Gray who was lucky to escape with just a conceded free-kick to his name.
There was drama when in the 73rd minute when Oliver was denied a run on goal by Forsdick. The last man, the Nuneaton man was duly forced to make the long walk back to the dressing rooms following an inevitable red card.
The free-kick was rolled into the path of Nicolau by Nutter and he saw his rasping drive give Collett no chance with the ball thumping against the back of the net via the trusty left peg of the City substitute.
Before play restarted Stephen O'Halloran replaced Wesley York for the visitors and when it did, Adam Walker was inches away with a low drive. Morgan then repeated the feat at the other end as things suddenly sprung to life.
With the game in its last 10 minutes a Nicolau free-kick led to a City corner and when the flag-kick was played in deep, there at the back post was Tom Miller to bundle home from close range to put the Imps in front for the first time.
It was very nearly 3-1 shortly after the restart when Taylor chipped over the advancing Collett before Larkin saw his follow-up effort somehow blocked by Cowan
A double Nuneaton switch then saw Robert Thompson-Brown and ex-Imp Kyle Perry replace Ben Ford and Andy Brown. Sponsors' 'Man of the Match' Dan Gray then had a shot charged down from the edge of the box.
In the first of four added minutes Nicolau was denied a second by a fine Collett save but when the corner was played in a foul on Taylor by Gordon gave the Imps a chance to put the game to bed from the penalty spot. Taylor took the responsibility himself from 12 yards but blasted straight against the crossbar before the ball bounced to a Nuneaton man.
FT: Imps 2 Nuneaton 1
City: Paul Farman, Dan Gray, Andrew Boyce, Tom Miller, John Nutter, David Morgan, Mamadou Fofana, Adam Smith, Jake Sheridan, Vadaine Oliver, Conner Robinson.
subs: Jamie Taylor (for Robinon 66), Nicky Nicolau (for Sheridan 66), Graham Hutchison, Colin Larkin (for Smith 66), Jake Turner.
bookings: Miller (11), Boyce (66)
goals: Nicolau (74), Miller (82)
Nuneaton: Neil Collett, Delroy Gordon, Gavin Cowan, Gareth Dean, James Armson, Adam Walker, Daniel Sleath, Ben Ford, Simon Forsdick, Wesley York, Andy Brown.
subs: Kyle Perry (for Ford 85) , Tom James, Robert Thompson-Brown (for Brown 85), Stephen O'Halloran (for York 74), Ben McNamara.
goals: Armson (3)
bookings: Ford (51)
sent off: Forsdick (73)
Referee: Chris Knowles
Assistants: Jonathan Burridge & George Sprague
Fourth Official: Gareth Mellor
Attendance: 1,579 (93 visiting supporters)